[R] Mixed effects model with a phylogenetic tree/ distance matrix as a random effect
bbolker at gmail.com
Mon Jun 3 22:22:45 CEST 2013
Bert Gunter <gunter.berton <at> gene.com> writes:
> Recommendation: Post this to the R-sig-mixed-models list, not here.
Seconded. Alternatively you could try the r-sig-phylo at r-project.org
mailing list, although I think I would try R-s-m-m first.
> On Mon, Jun 3, 2013 at 9:27 AM, Roey Angel
> <angel <at> mpi-marburg.mpg.de> wrote:
> > Hi,
> > I'm trying to build a mixed-effects model in which I'd like to include
> > either a distance matrix or a phylogenetic tree as a random effect.
> > The troubles I've had are that:
> > 1. Function lmer() in package lme4 only accepts a data frame column
> as a
> > random factor and not a distance matrix.
This is not going to change in the near future, although
there is a 'pedigreemm' package built on lme4 that
might do what you want.
You might be able to use MASS::glmmPQL in conjunction with
the corStruct structures from nlme (for classical geostatistical
correlation models); ape (for phylogenetic models); or ramps (other
INLA might ??? allow tree correlation structures:
Ives and Garland have some MATLAB code for phylogenetic
logistic regression ...
> > 2. Function MCMCglmm() in package MCMCglmm only accepts a rooted and
> > ultrametric phylogenetic tree as a pedigree argument while my tree is
> > neither (and for various reasons I cannot construct one or
> coerce mine to be
> > a rooted, ultrametric tree).
> > Is there any way around it?
> > I'd appreciate mostly a solution to problem 1.
> > Roey
> > --
> > Dr. Roey Angel
> > Max-Planck-Institute for Terrestrial Microbiology
> > Karl-von-Frisch-Strasse 10
> > D-35043 Marburg, Germany
> > Office: +49 (0)6421/178-832
> > Mobile: +49 (0)176/612-785-88
> > ______________________________________________
> > R-help <at> r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
More information about the R-help